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normal Segmentation Fault during PR run

  • think_beyond
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11 years 8 months ago #1069 by think_beyond
Segmentation Fault during PR run was created by think_beyond
Hello Colleagues,

I am very new to CG.

I am following Protein in Water tutorial.

I was successful until the position restraint run. My run crashes with an error message 'Segmentation Fault (Core Dumped).
Following is my mdp file.

integrator = md
define = -DPOSRES
tinit = 0.0
dt = 0.02
nsteps = 5000
nstcomm = 1
comm-grps =

nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 1000
nstenergy = 100
nstxtcout = 100
xtc_precision = 100
xtc-grps =
energygrps = Protein

nstlist = 10
ns_type = grid
pbc = xyz
rlist = 1.4

coulombtype = Shift
rcoulomb_switch = 0.0
rcoulomb = 1.2
epsilon_r = 15
vdw_type = Shift
rvdw_switch = 0.9
rvdw = 1.2
DispCorr = No

tcoupl = V-rescale
tc-grps = system
tau_t = 1.0
ref_t = 320
Pcoupl = Berendsen
Pcoupltype = isotropic
tau_p = 3.0
compressibility = 3e-4
ref_p = 1.0

gen_vel = no
gen_temp = 320
gen_seed = 473529

constraints = none
constraint_algorithm = Lincs
unconstrained_start = no
lincs_order = 4
lincs_warnangle = 30

An my commands were these,

$ grompp -f pr.mdp -c solvated.gro -r solvated.gro -o cg_pr.tpr -p system.top

$ mdrun -v -s cg_pr.tpr -o cg_pr.trr -c cg_pr.gro -e cg_pr.edr -g cg_pr.log > & cg_pr.job &


Can anyone find out the problem here?

Thanks,

Peterson J

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11 years 8 months ago #1070 by djurre
Replied by djurre on topic Segmentation Fault during PR run
Most likely your system is not properly energy minimized. Make sure the potential energy and force go down properly during the EM.

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11 years 8 months ago #1076 by think_beyond
Replied by think_beyond on topic Segmentation Fault during PR run
Thanks Djurre,

Now the PR run runs successfully but with the following warning.

Step 1 Warning: pressure scaling more than 1%, mu: 0.987573 0.987573 0.987573

Step 1 Warning: pressure scaling more than 1%, mu: 0.987573 0.987573 0.987573

Step 1 Warning: pressure scaling more than 1%, mu: 0.987573 0.987573 0.987573

NOTE: Turning on dynamic load balancing


What does this warning really mean? Is fine to proceed with no action to this warning?

Peterson J

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11 years 8 months ago #1078 by djurre
Replied by djurre on topic Segmentation Fault during PR run
The message means the system is shrinking "a lot" in the first step. (a lot means 1.25% in every dimension and it is not a lot at all). It is due to the system not being relaxed yet (and that is why you run the PR-run). So this is perfectly fine.

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